Hi,
it looks like the patch wasn't applied. I've actually committed the
bug fix to CRAN where aroma.core v1.8.1 is now available. If you do
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
that one should install (and any patches will be dropped).
Let me know if you still have problems
/Henrik
On Mon, Dec 6, 2010 at 4:54 AM, Hans-Ulrich
<hans-ulrich.kl...@uni-muenster.de> wrote:
> Hi Hendrik,
>
> I installed the patches and removed the report and the cbs folder.
> Then, I run the segmentation and the chromosome explorer again. I got
> the same/similar error message (see below). The error occured when
> processing the second sample so the first one seems to run without
> problems.
> Can I run the chromosome explorer and exclude chromosome 25?
>
> Regards,
> Hans-Ulrich
>
> 20101206 12:53:52| Plotting S2 for chromosome 24 [NAMB]...done
> 20101206 12:53:52| Calling onFit.CopyNumberSegmentationModel()
> hooks...done
> 20101206 12:53:52|Array #2 ('S2') of 4 on chromosome 24...done
> 20101206 12:53:52|Array #2 ('S2') of 4 on chromosome 25...
> 20101206 12:53:52| Loading results from file...
> 20101206 12:53:52| Pathname: cbsData/Koschmieder,ACC,ra,-XY,BPN,-
> XY,RMA,A+B,FLN,-XY,paired/MOUSEDIVm520650/
> S2,chr25,9012c8079b8a75fe8fc388ca02bfb65e.xdr
> 20101206 12:53:52| Fit object: DNAcopy
> 20101206 12:53:52| Loading results from file...done
> 20101206 12:53:52| Calling onFit.CopyNumberSegmentationModel()
> hooks...
> ERROR caught in onFit.CopyNumberSegmentationModel():
> [2010-12-06 12:53:53] Exception: Cannot infer number of bases in
> chromosome. No such chromosome: 25
> at throw(Exception(...))
> at throw.default("Cannot infer number of bases in chromosome. No
> such chromoso
> at throw("Cannot infer number of bases in chromosome. No such
> chromosome: ", c
> at getChromosomeLength(chromosome)
> at doTryCatch(return(expr), name, parentenv, handler)
> at tryCatchOne(expr, names, parentenv, handlers[[1]])
> at tryCatchList(expr, classes, parentenv, handlers)
> at tryCatch({
> at fcn(...)
> at doTryCatch(return(expr), name, parentenv, handler)
> at tryCatchOne(expr, names, parentenv, handlers[[1]])
> at tryCatchList(expr, classes, parentenv, handlers)
> at tryCatch({
> at callHooks.list(hooks, ...)
> at callHooks(hooks, ...)
> at callHooks.default(hookName, fit = fit, chromosome = chr, fullname
> = fullnam
> at callHooks(hookName, fit = fit, chromosome = chr, fullname =
> fullname)
> at fit.CopyNumberSegmentationModel(this, ..., .retResults = FALSE,
> verbose = v
> at fit(this, ..., .retResults = FALSE, verbose = verbose)
> at plot.CopyNumberSegmentationModel(model, path = path, imageFormat
> = "png", p
> at plot(model, path = path, imageFormat = "png", plotband =
> plotband, arrays =
> at writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes
> = chromos
> at writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
> zooms = zooms
> at process.ChromosomeExplorer(ce, verbose = verbose)
> at process(ce, verbose = verbose)
> used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 1178686 63 4079505 217.9 26615696 1421.5
> Vcells 1568318 12 4818496 36.8 41974408 320.3
> 20101206 12:53:53| Calling onFit.CopyNumberSegmentationModel()
> hooks...done
> 20101206 12:53:53|Calling onFit.CopyNumberSegmentationModel()
> hooks...done
> Error in list(`process(ce, verbose = verbose)` = <environment>,
> `process.ChromosomeExplorer(ce, verbose = verbose)` =
> <environment>, :
>
> [2010-12-06 12:53:53] Exception: Cannot exit(): Argument 'indent'
> makes 'indentPos' negative: -1
> at throw(Exception(...))
> at throw.default("Cannot exit(): Argument 'indent' makes 'indentPos'
> negative:
> at throw("Cannot exit(): Argument 'indent' makes 'indentPos'
> negative: ", this
> at exit.Verbose(verbose)
> at exit(verbose)
> at fit.CopyNumberSegmentationModel(this, ..., .retResults = FALSE,
> verbose = v
> at fit(this, ..., .retResults = FALSE, verbose = verbose)
> at plot.CopyNumberSegmentationModel(model, path = path, imageFormat
> = "png", p
> at plot(model, path = path, imageFormat = "png", plotband =
> plotband, arrays =
> at writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes
> = chromos
> at writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
> zooms = zooms
> at process.ChromosomeExplorer(ce, verbose = verbose)
> at process(ce, verbose = verbose)
> Error in list(`process(ce, verbose = verbose)` = <environment>,
> `process.ChromosomeExplorer(ce, verbose = verbose)` =
> <environment>, :
>
> [2010-12-06 12:53:53] Exception: Cannot exit(): Argument 'indent'
> makes 'indentPos' negative: -1
> at throw(Exception(...))
> at throw.default("Cannot exit(): Argument 'indent' makes 'indentPos'
> negative:
> at throw("Cannot exit(): Argument 'indent' makes 'indentPos'
> negative: ", this
> at exit.Verbose(this)
> at exit(this)
> at popState.Verbose(verbose)
> at popState(verbose)
> at throw.Exception(Exception(...))
> at throw(Exception(...))
> at throw.default("Cannot exit(): Argument 'indent' makes 'indentPos'
> negative:
> at throw("Cannot exit(): Argument 'indent' makes 'indentPos'
> negative: ", this
> at exit.Verbose(verbose)
> at exit(verbose)
> at fit.CopyNumberSegmentationModel(this, ..., .retResults = FALSE,
> verbose = v
> at fit(this, ..., .retResults = FALSE, verbose = verbose)
> at plot.CopyNumberSegmentationModel(model, path = path, imageFormat
> = "png", p
> at plot(model, path = path, imageFormat = "png", plotband =
> plotband, arrays =
> at writeGraphs.ChromosomeExplore
> 20101206 12:53:53|Generating ChromosomeExplorer report...done
>
>
>
>
> On Dec 3, 8:09 am, Henrik Bengtsson <henrik.bengts...@aroma-
> project.org> wrote:
>> Hi,
>>
>> I could reproduce this error (also on the Human genome when trying to
>> generate CE plots for Chr25). It's a bug, which I have patched (until
>> next release). Run the following and the patches will be installed
>> too:
>>
>> source("http://aroma-project.org/hbLite.R";);
>> hbInstall("aroma.affymetrix");
>>
>> Let me know if it solves your problem.
>>
>> /Henrik
>>
>> On Wed, Dec 1, 2010 at 2:28 PM, Hans-Ulrich
>>
>> <hans-ulrich.kl...@uni-muenster.de> wrote:
>> > Sorry, I forgot that:
>>
>> >> sessionInfo()
>> > R version 2.12.0 (2010-10-15)
>> > Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> > locale:
>> > [1] C
>>
>> > attached base packages:
>> > [1] stats graphics grDevices utils datasets methods
>> > base
>>
>> > other attached packages:
>> > [1] Cairo_1.4-5 RColorBrewer_1.0-2
>> > DNAcopy_1.24.0
>> > [4] preprocessCore_1.12.0 sfit_0.1.9
>> > aroma.affymetrix_1.8.1
>> > [7] aroma.apd_0.1.7 affxparser_1.22.0
>> > R.huge_0.2.0
>> > [10] aroma.core_1.8.0 aroma.light_1.18.2
>> > matrixStats_0.2.2
>> > [13] R.rsp_0.4.0 R.cache_0.3.0
>> > R.filesets_0.9.1
>> > [16] digest_0.4.2 R.utils_1.5.8
>> > R.oo_1.7.4
>> > [19] R.methodsS3_1.2.1
>>
>> > loaded via a namespace (and not attached):
>> > [1] tools_2.12.0
>> > Warning message:
>> > 'DESCRIPTION' file has 'Encoding' field and re-encoding is not
>> > possible
>>
>> > Regards,
>> > Hans-Ulrich
>>
>> > On Dec 1, 6:44 pm, Henrik Bengtsson <henrik.bengts...@aroma-
>> > project.org> wrote:
>> >> Hi,
>>
>> >> before anything else, are you running the latest aroma.affymetrix
>> >> (v1.8.0), i.e. what's your sessionInfo()?
>>
>> >> /Henrik
>>
>> >> On Wed, Dec 1, 2010 at 9:32 AM, Hans-Ulrich
>>
>> >> <hans-ulrich.kl...@uni-muenster.de> wrote:
>> >> > Hi Hendrik,
>>
>> >> > I created a file for the mouse genome. However, I still get an error
>> >> > message:
>>
>> >> >> cbs = CbsModel(cesNSamples, cesNControls, genome="Mouse")
>> >> >> df <- getGenomeData(cbs, verbose=verbose)
>> >> > 20101201 14:44:53|Reading genome chromosome annotation file...
>> >> > 20101201 14:44:53| Searching for the file...
>> >> > 20101201 14:44:54| Searching for the file...done
>> >> > 20101201 14:44:54| Reading data file...
>> >> > 20101201 14:44:54| Pathname: annotationData/genomes/Mouse/
>> >> > Mouse,chromosomes.txt
>> >> > 20101201 14:44:54| Reading data file...done
>> >> > 20101201 14:44:54| Translating chromosome names...
>> >> > 20101201 14:44:54| Translating chromosome names...done
>> >> > 20101201 14:44:54|Reading genome chromosome annotation file...done
>> >> >> df
>> >> > nbrOfBases nbrOfGenes
>> >> > 1 197195432 1237
>> >> > 2 181748087 1779
>> >> > 3 159599783 1046
>> >> > 4 155630120 1286
>> >> > 5 152537259 1285
>> >> > 6 149517037 1158
>> >> > 7 152524553 1975
>> >> > 8 131738871 1082
>> >> > 9 124076172 1260
>> >> > 10 129993255 1036
>> >> > 11 121843856 1606
>> >> > 12 121257530 712
>> >> > 13 120284312 850
>> >> > 14 125194864 860
>> >> > 15 103494974 823
>> >> > 16 98319150 679
>> >> > 17 95272651 1075
>> >> > 18 90772031 522
>> >> > 19 61342430 739
>> >> > 23 166650296 800
>> >> > 24 15902555 12
>> >> > M 16299 13
>> >> >> fit(cbs, min.width=5, verbose=verbose)
>> >> >> ce = ChromosomeExplorer(cbs)
>> >> >> process(ce, verbose=verbose)
>> >> > [...]
>> >> > ERROR caught in onFit.CopyNumberSegmentationModel():
>> >> > [2010-12-01 18:18:04] Exception: Cannot infer number of bases in
>> >> > chromosome. No such chromosome: 25
>> >> > at throw(Exception(...))
>> >> > at throw.default("Cannot infer number of bases in chromosome. No
>> >> > such chromoso
>> >> > at throw("Cannot infer number of bases in chromosome. No such
>> >> > chromosome: ", c
>> >> > at getChromosomeLength(chromosome)
>> >> > at doTryCatch(return(expr), name, parentenv, handler)
>> >> > at tryCatchOne(expr, names, parentenv, handlers[[1]])
>> >> > at tryCatchList(expr, classes, parentenv, handlers)
>> >> > [...]
>>
>> >> > Do I have to rename chromosome "M" to "25"?
>>
>> >> > Best wishes,
>> >> > Hans-Ulrich
>>
>> >> > On Nov 9, 10:20 pm, Henrik Bengtsson <henrik.bengts...@aroma-
>> >> > project.org> wrote:
>> >> >> More below...
>>
>> >> >> On Tue, Nov 9, 2010 at 1:16 PM, Henrik Bengtsson
>>
>> >> >> <henrik.bengts...@aroma-project.org> wrote:
>> >> >> > Hi.
>>
>> >> >> > On Tue, Nov 9, 2010 at 3:37 AM, Hans-Ulrich
>> >> >> > <hans-ulrich.kl...@uni-muenster.de> wrote:
>> >> >> >> Hi Henrik,
>>
>> >> >> >> thank you very much for your help! I tried your code and it seemed
>> >> >> >> that I got reasonable results. I will compare the results to the
>> >> >> >> results from the Affymetrix software later, but it looks well at a
>> >> >> >> first glance.
>>
>> >> >> >> I have two other questions/remarks:
>> >> >> >> 1) The data.frames returned by getRegions() on the segmented copy
>> >> >> >> numbers contains links to the human genome and not to the mouse
>> >> >> >> genome.
>>
>> >> >> > That's unfortunately still hardwired and has to be manually edited
>> >> >> > afterwards.
>>
>> >> >> >> 2) The ChromosomeExplorer() method does not work and it looks as if
>> >> >> >> the methods tries to generate plots for the human genome.
>>
>> >> >> > Does the "and" mean "because" here or are there two different
>> >> >> > problems?
>>
>> >> >> >> Both issues are not serious and I could fix 1) quickly using the
>> >> >> >> gsub
>> >> >> >> command. However, can I pass the mouse genome as parameter or are
>> >> >> >> these functions implemented for the human genome only?
>>
>> >> >> > It is possible to specify which genome the segmentation method should
>> >> >> > use and hence ChromosomeExplorer. For this to work you need to
>> >> >> > provide correctly formatted genome annotation data under
>> >> >> > annotationData/genomes/<GenomeName>/. For an example of such a file,
>> >> >> > see
>>
>> >> >> > path <- system.file("annotationData/genomes/Human",
>> >> >> > package="aroma.core");
>> >> >> > filename <- "Human,chromosomes.txt";
>> >> >> > pathname <- file.path(path, filename);
>> >> >> > file.show(pathname);
>>
>> >> >> > Also, have a look at thread 'Custom Canine SNP (DogSty06m520431);
>> >> >> > problem with chr24-39 Options' started on August 23, 2010:
>>
>> >> >> > https://groups.google.com/group/aroma-affymetrix/browse_thread/thread...
>>
>> >> >> BTW, a good test to make sure it works for your genome, verify that
>> >> >> something like this works:
>>
>> >> >> > db <- AromaGenomeTextFile$byGenome("Human");
>> >> >> > print(db);
>>
>> >> >> AromaGenomeTextFile:
>> >> >> Name: Human
>> >> >> Tags: chromosomes
>> >> >> Full name: Human,chromosomes
>> >> >> Pathname: annotationData/genomes/Human/Human,chromosomes.txt
>> >> >> File size: 477 bytes
>> >> >> RAM: 0.01 MB
>> >> >> Number of data rows: 25
>> >> >> Columns [3]: 'chromosome', 'nbrOfBases', 'nbrOfGenes'
>> >> >> Number of text lines: 26> data <- readDataFrame(db);
>> >> >> > print(data);
>>
>> >> >> chromosome nbrOfBases nbrOfGenes
>> >> >> 1 1 245203898 2968
>> >> >> 2 2 243315028 2288
>> >> >> 3 3 199411731 2032
>> >> >> 4 4 191610523 1297
>> >> >> 5 5 180967295 1643
>> >> >> 6 6 170740541 1963
>> >> >> 7 7 158431299 1443
>> >> >> 8 8 145908738 1127
>> >> >> 9 9 134505819 1299
>> >> >> 10 10 135480874 1440
>> >> >> 11 11 134978784 2093
>> >> >> 12 12 133464434 1652
>> >> >> 13 13 114151656 748
>> >> >> 14 14 105311216 1098
>> >> >> 15 15 100114055 1122
>> >> >> 16 16 89995999 1098
>> >> >> 17 17 81691216 1576
>> >> >> 18 18 77753510 766
>> >> >> 19 19 63790860 1454
>> >> >> 20 20 63644868 927
>> >> >> 21 21 46976537 303
>> >> >> 22 22 49476972 288
>> >> >> 23 X 152634166 1184
>> >> >> 24 Y 50961097 231
>> >> >> 25 M 16569 37
>>
>> >> >> /Henrik
>>
>> >> >> > Hope this helps
>>
>> >> >> > Henrik
>>
>> >> >> >> Best wishes,
>> >> >> >> Hans-Ulrich
>>
>> >> >> >> On Nov 5, 11:20 pm, Henrik Bengtsson <henrik.bengts...@aroma-
>> >> >> >> project.org> wrote:
>> >> >> >>> Hi.
>>
>> >> >> >>> On Fri, Nov 5, 2010 at 9:09 AM, Hans-Ulrich
>>
>> >> >> >>> <hans-ulrich.kl...@uni-muenster.de> wrote:
>> >> >> >>> > Hi all,
>>
>> >> >> >>> > I am using the Affymetrix "MOUSEDIVm520650" chip. During the the
>> >> >> >>> > normalization step for fragment length, the aroma software
>> >> >> >>> > complains
>> >> >> >>> > that no probes for enzyme 1 only exist (the same for enzyme 2). I
>> >> >> >>> > found
>> >> >> >>> > this discussion:
>> >> >> >>> >http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/...
>>
>> >> >> >>> > In the NetAffx annotation files, all probes have fragment length
>> >> >> >>> > for
>> >> >> >>> > both enzymes, although they are sometimes quite large. The
>> >> >> >>> > affymetrix
>> >> >> >>> > protocol says that the PCR works well for fragments between 200
>> >> >> >>> > and
>> >> >> >>> > 1100bps. The annotation files for the Genome Wide SNP 6.0 arrays
>> >> >> >>> > annotate fragments up to 2000bps.
>>
>> >> >> >>> > To use the aroma software, I want to modify the ufl file and set
>> >> >> >>> > all
>> >> >> >>> > fragment length entries < 45 or > 2000 to NA. Unfortunately, I
>> >> >> >>> > have
>> >> >> >>> > no
>> >> >> >>> > plan how to do this. Can someone point me to appropriate
>> >> >> >>> > documentation?
>>
>> >> >> >>> The how-to page 'Create a Unit Fragment Length (UFL) file' at
>>
>> >> >> >>> http://aroma-project.org/howtos/CreateAUnitFragmentLengthFile
>>
>> >> >> >>> should be useful. Make sure to not update the original UFL file,
>> >> >> >>> but
>> >> >> >>> instead a renamed copy of it.
>>
>> >> >> >>> Bah, it's easier if I just write it:
>>
>> >> >> >>> # Get the UFL file
>> >> >> >>> chipType <- "MOUSEDIVm520650";
>> >> >> >>> ufl <- AromaUflFile$byChipType(chipType);
>>
>> >> >> >>> # Get the pathname of the source file
>> >> >> >>> pathname <- getPathname(ufl);
>>
>> >> >> >>> #
>>
>> ...
>>
>> read more »
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
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>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
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